Banani, S. F., Lee, H. O., Hyman, A. A. & Rosen, M. K. Biomolecular condensates: organizers of cellular biochemistry. Nat. Rev. Mol. Cell Biol. 18, 285–298 (2017).
Google Scholar
Hyman, A. A., Weber, C. A. & Jülicher, F. Liquid–liquid phase separation in biology. Annu. Rev. Cell Dev. Biol. 30, 39–58 (2014).
Google Scholar
Corbet, G. A. & Parker, R. RNP granule formation: lessons from P-bodies and stress granules. Cold Spring Harb. Symp. Quant. Biol. 84, 203–215 (2019).
Google Scholar
Roden, C. & Gladfelter, A. S. RNA contributions to the form and function of biomolecular condensates. Nat. Rev. Mol. Cell Biol. 22, 183–195 (2021).
Google Scholar
Elguindy, M. M. et al. PUMILIO, but not RBMX, binding is required for regulation of genomic stability by noncoding RNA NORAD. eLife 8, e48625 (2019).
Google Scholar
Kopp, F. et al. PUMILIO hyperactivity drives premature aging of Norad-deficient mice. eLife 8, e42650 (2019).
Google Scholar
Lee, S. et al. Noncoding RNA NORAD regulates genomic stability by sequestering PUMILIO proteins. Cell 164, 69–80 (2016).
Google Scholar
Tichon, A. et al. A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells. Nat. Commun. 7, 12209 (2016).
Google Scholar
Pandya-Jones, A. et al. A protein assembly mediates Xist localization and gene silencing. Nature 587, 145–151 (2020).
Google Scholar
Hacisuleyman, E., Shukla, C. J., Weiner, C. L. & Rinn, J. L. Function and evolution of local repeats in the Firre locus. Nat. Commun. 7, 11021 (2016).
Google Scholar
Yamazaki, T. et al. Functional domains of NEAT1 architectural lncRNA induce paraspeckle assembly through phase separation. Mol. Cell 70, 1038–1053.e7 (2018).
Google Scholar
Lin, Y., Protter, D. S., Rosen, M. K. & Parker, R. Formation and maturation of phase-separated liquid droplets by RNA-binding proteins. Mol. Cell 60, 208–219 (2015).
Google Scholar
Quinn, J. J. & Chang, H. Y. Unique features of long non-coding RNA biogenesis and function. Nat. Rev. Genet. 17, 47–62 (2016).
Google Scholar
Kopp, F. & Mendell, J. T. Functional classification and experimental dissection of long noncoding RNAs. Cell 172, 393–407 (2018).
Google Scholar
Yao, R. W., Wang, Y. & Chen, L. L. Cellular functions of long noncoding RNAs. Nat. Cell Biol. 21, 542–551 (2019).
Google Scholar
Goldstrohm, A. C., Hall, T. M. T. & McKenney, K. M. Post-transcriptional regulatory functions of mammalian Pumilio proteins. Trends Genet. 34, 972–990 (2018).
Google Scholar
Khong, A. et al. The stress granule transcriptome reveals principles of mRNA accumulation in stress granules. Mol. Cell 68, 808–820.e5 (2017).
Google Scholar
Namkoong, S., Ho, A., Woo, Y. M., Kwak, H. & Lee, J. H. Systematic characterization of stress-induced RNA granulation. Mol. Cell 70, 175–187.e8 (2018).
Google Scholar
Zhang, H. et al. RNA controls polyQ protein phase transitions. Mol. Cell 60, 220–230 (2015).
Google Scholar
Edwards, T. A., Pyle, S. E., Wharton, R. P. & Aggarwal, A. K. Structure of Pumilio reveals similarity between RNA and peptide binding motifs. Cell 105, 281–289 (2001).
Google Scholar
Litke, J. L. & Jaffrey, S. R. Highly efficient expression of circular RNA aptamers in cells using autocatalytic transcripts. Nat. Biotechnol. 37, 667–675 (2019).
Google Scholar
Gennarino, V. A. et al. A mild PUM1 mutation is associated with adult-onset ataxia, whereas haploinsufficiency causes developmental delay and seizures. Cell 172, 924–936.e11 (2018).
Google Scholar
Gennarino, V. A. et al. Pumilio1 haploinsufficiency leads to SCA1-like neurodegeneration by increasing wild-type Ataxin1 levels. Cell 160, 1087–1098 (2015).
Google Scholar
D’Amico, D. et al. The RNA-binding protein PUM2 impairs mitochondrial dynamics and mitophagy during aging. Mol. Cell 73, 775–787.e10 (2019).
Google Scholar
Klosin, A. et al. Phase separation provides a mechanism to reduce noise in cells. Science 367, 464–468 (2020).
Google Scholar
Islam, S. et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res. 21, 1160–1167 (2011).
Google Scholar
Marinov, G. K. et al. From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. Genome Res. 24, 496–510 (2014).
Google Scholar
Shapiro, E., Biezuner, T. & Linnarsson, S. Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat. Rev. Genet. 14, 618–630 (2013).
Google Scholar
Golden, R. J. et al. An Argonaute phosphorylation cycle promotes microRNA-mediated silencing. Nature 542, 197–202 (2017).
Google Scholar
Randolph, L. N., Bao, X., Zhou, C. & Lian, X. An all-in-one, Tet-On 3G inducible PiggyBac system for human pluripotent stem cells and derivatives. Sci. Rep. 7, 1549 (2017).
Google Scholar
Mito, M., Kawaguchi, T., Hirose, T. & Nakagawa, S. Simultaneous multicolor detection of RNA and proteins using super-resolution microscopy. Methods 98, 158–165 (2016).
Google Scholar
Bolte, S. & Cordelières, F. P. A guided tour into subcellular colocalization analysis in light microscopy. J. Microsc. 224, 213–232 (2006).
Google Scholar
Costes, S. V. et al. Automatic and quantitative measurement of protein-protein colocalization in live cells. Biophys. J. 86, 3993–4003 (2004).
Google Scholar
Wheeler, J. R., Matheny, T., Jain, S., Abrisch, R. & Parker, R. Distinct stages in stress granule assembly and disassembly. eLife 5, e18413 (2016).
Google Scholar
Frankish, A. et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 47, D766–D773 (2019).
Google Scholar
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Google Scholar
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).
Google Scholar
McCarthy, D. J., Chen, Y. & Smyth, G. K. Differential expression analysis of multifactor RNA-seq experiments with respect to biological variation. Nucleic Acids Res. 40, 4288–4297 (2012).
Google Scholar
Hafner, M. et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141, 129–141 (2010).
Google Scholar